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Results: 1 to 20 of 99

1.

Generalized Born forces: surface integral formulation.

Fogolari F, Corazza A, Esposito G.

J Chem Phys. 2013 Feb 7;138(5):054112. doi: 10.1063/1.4789537.

PMID:
23406103
[PubMed - indexed for MEDLINE]
2.

A differential equation for the Generalized Born radii.

Fogolari F, Corazza A, Esposito G.

Phys Chem Chem Phys. 2013 Jun 28;15(24):9783-91. doi: 10.1039/c3cp51174j.

PMID:
23676843
[PubMed - indexed for MEDLINE]
3.

Treecode-based generalized Born method.

Xu Z, Cheng X, Yang H.

J Chem Phys. 2011 Feb 14;134(6):064107. doi: 10.1063/1.3552945.

PMID:
21322661
[PubMed - indexed for MEDLINE]
4.

FACTS: Fast analytical continuum treatment of solvation.

Haberthür U, Caflisch A.

J Comput Chem. 2008 Apr 15;29(5):701-15.

PMID:
17918282
[PubMed - indexed for MEDLINE]
5.

Analysis of integral expressions for effective Born radii.

Mongan J, Svrcek-Seiler WA, Onufriev A.

J Chem Phys. 2007 Nov 14;127(18):185101.

PMID:
18020664
[PubMed - indexed for MEDLINE]
6.

Bluues: a program for the analysis of the electrostatic properties of proteins based on generalized Born radii.

Fogolari F, Corazza A, Yarra V, Jalaru A, Viglino P, Esposito G.

BMC Bioinformatics. 2012 Mar 28;13 Suppl 4:S18. doi: 10.1186/1471-2105-13-S4-S18.

PMID:
22536964
[PubMed - indexed for MEDLINE]
Free PMC Article
7.

Secondary structure bias in generalized Born solvent models: comparison of conformational ensembles and free energy of solvent polarization from explicit and implicit solvation.

Roe DR, Okur A, Wickstrom L, Hornak V, Simmerling C.

J Phys Chem B. 2007 Feb 22;111(7):1846-57. Epub 2007 Jan 27.

PMID:
17256983
[PubMed - indexed for MEDLINE]
8.

A strategy for reducing gross errors in the generalized Born models of implicit solvation.

Onufriev AV, Sigalov G.

J Chem Phys. 2011 Apr 28;134(16):164104. doi: 10.1063/1.3578686.

PMID:
21528947
[PubMed - indexed for MEDLINE]
Free PMC Article
9.

Differential geometry based solvation model II: Lagrangian formulation.

Chen Z, Baker NA, Wei GW.

J Math Biol. 2011 Dec;63(6):1139-200. doi: 10.1007/s00285-011-0402-z. Epub 2011 Jan 30.

PMID:
21279359
[PubMed - indexed for MEDLINE]
Free PMC Article
10.

Multiscale generalized born modeling of ligand binding energies for virtual database screening.

Liu HY, Grinter SZ, Zou X.

J Phys Chem B. 2009 Sep 3;113(35):11793-9. doi: 10.1021/jp901212t.

PMID:
19678651
[PubMed - indexed for MEDLINE]
Free PMC Article
11.

Implicit solvation based on generalized Born theory in different dielectric environments.

Feig M, Im W, Brooks CL 3rd.

J Chem Phys. 2004 Jan 8;120(2):903-11.

PMID:
15267926
[PubMed - indexed for MEDLINE]
12.
13.

Generalized born model with a simple smoothing function.

Im W, Lee MS, Brooks CL 3rd.

J Comput Chem. 2003 Nov 15;24(14):1691-702.

PMID:
12964188
[PubMed - indexed for MEDLINE]
14.

Numerical solution of boundary-integral equations for molecular electrostatics.

Bardhan JP.

J Chem Phys. 2009 Mar 7;130(9):094102. doi: 10.1063/1.3080769.

PMID:
19275391
[PubMed - indexed for MEDLINE]
15.

Effective Born radii in the generalized Born approximation: the importance of being perfect.

Onufriev A, Case DA, Bashford D.

J Comput Chem. 2002 Nov 15;23(14):1297-304.

PMID:
12214312
[PubMed - indexed for MEDLINE]
16.
17.

Energetic decomposition with the generalized-born and Poisson-Boltzmann solvent models: lessons from association of G-protein components.

Carrascal N, Green DF.

J Phys Chem B. 2010 Apr 22;114(15):5096-116. doi: 10.1021/jp910540z.

PMID:
20355699
[PubMed - indexed for MEDLINE]
18.

Assessing implicit models for nonpolar mean solvation forces: the importance of dispersion and volume terms.

Wagoner JA, Baker NA.

Proc Natl Acad Sci U S A. 2006 May 30;103(22):8331-6. Epub 2006 May 18. Erratum in: Proc Natl Acad Sci U S A. 2007 Jan 30;104(5):1732.

PMID:
16709675
[PubMed - indexed for MEDLINE]
Free PMC Article
19.

Calculating solvation energies by means of a fluctuating charge model combined with continuum solvent model.

Zhao DX, Yu L, Gong LD, Liu C, Yang ZZ.

J Chem Phys. 2011 May 21;134(19):194115. doi: 10.1063/1.3590718.

PMID:
21599052
[PubMed - indexed for MEDLINE]
20.

Exploring protein native states and large-scale conformational changes with a modified generalized born model.

Onufriev A, Bashford D, Case DA.

Proteins. 2004 May 1;55(2):383-94.

PMID:
15048829
[PubMed - indexed for MEDLINE]

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